I believe there is more than a 0.1% error in fill to fill variations. Especially if you fill at different pumps. Although I believe they measure fuel accurately, I do not think they will all stop at the same level. Also, since a fuel tank is an irregular conainer, if your car is tilted in different ways, the error can easilly go past 0.1%.
You should try to do
coastdown tests to validate the manufacturers value you input in your model (Cd and Crr). Maybe
revalidate the frontal area too. As already suggested, you could validate you fuel measurements from MAF and O2 sensor output.
Also, Crr gets lower as the distance driven increase (as the tire gets hotter, hysteresis losses are reduced). There are a lot of other variables that will change like that depending on the trips you log.